Short Description

Ensemble of blocks that implement SODA method for confocal and super-resolution microscopy, in 2 and 3 dimensions

Team: Bio Image Analysis
Institution: Institut Pasteur
Website: http://icy.bioimageanalysis.org/

Documentation

This plugin contains 4 functional and independent blocks that performs SODA analysis in standard (widefield, confocal, structured-illumination…) and localization-based (STORM, PALM, DNA-PAINT…) microscopy.

Details of the method and algorithm are given in

– Block SODA

SODA block

Parameters:

List of detections 1 & 2: spots (ROIs) corresponding to detections from channel or sequence 1 & 2

Input sequences: respective sequences of detections 1 & 2. Input sequences are used to compute the intensity centers (i.e. positions) of detections 1 & 2

ROI of analysis (cell’s shape) This key parameter corresponds to the ROI where SODA analysis is performed. If this ROI is too large, detections might appear as coupled (colocalized) while they are not..

Max. Radius and Step Max distance and step for computing the Ripley’s K function (see original article for details)

Fixed search distance: If selected, the plugin will simply count the number of detections 2 at distances 0, step,..,i*step,..Max. radius from detections 1

Example of protocol:

Simple protocol analyzing the coupling between 2 populations of spots (a third channel is used to automatically determine the cell’s ROI)

Demo video Simple protocol

Simple protocol screenshot

 

Complete protocol (3 colors) used in original publication 

Demo video complete protocol (3 colors)

3 Color protocol

-Blocks SODA STORM 2D&3D

STORM 3D protocol

Demonstration video (STORM imaging and analysis)

Using the SODA STORM 3D protocol

STORM 2D protocol

-Block SODA suite

coming soon…

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Changelog

  • Version 1.0.6.0 • Released on: 2019-08-14 11:00:00
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    Description:

    Fixed plugins packaging so it correctly auto update (Stephane)

  • Version 1.0.5.0 • Released on: 2019-08-14 10:00:00
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    Description:

    Fixed issue with POI library update (Stephane)

  • Version 0.0.1.4 • Released on: 2018-08-12 21:48:23
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    Description:

    compatible with java 6

  • Version 0.0.1.3 • Released on: 2018-07-18 02:20:14
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    Description:

    Fixed some bugs on ROIs manipulation in Manders&Overlap coefficients computation (SODA suite bloc)

  • Version 0.0.1.2 • Released on: 2018-06-28 20:56:52
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  • Version 0.0.1.1 • Released on: 2018-02-28 22:25:42
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    Description:

    Fix bugs in trio block

  • Version 0.0.1.0 • Released on: 2018-02-23 18:30:02
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